You probably have Previews set to be the JPEGS from the camera, which means they have been adjusted to the camera's settings and look "finished." The NEF files are literally raw data and will require adjustment. RAW files should never look perfect.
Personally I shoot RAW+JPEG and recommend that.
When importing you can set Aperture to choose either the RAW or the JPEG files to use as Masters. Or you can do two imports and make a Project for the NEFs and a Project for the JPEGs. That can be very convenient because the JPEGs are ready for instant review/usage while the NEFs are there for further post-processing as needed.
Note that in my comments raw=RAW=NEF. I tend to use the terms interchangeably.
I read some files and there mentioned that some NEF has a plug-in JPEG pic. I don't really know since I used RAW only before. Anyhow, I'll turn to RAW + JPG mode. Thanks again for the advice!
But indeed, it made me no happy. I think apple should do something. I will do the adjustments on "real" NEFs, which should be the most close to what I saw while shooting. The situation now is far from my expectation.
How can a general software with general CPU/GPU's MAC be defeated by a small and simple processor and program on a digital camera? And even there's no way to report the problem... This is definately not enough to customers.
Nothing has been destroyed. What you're seeing is the result of Aperture's inability to respond to Picture Control settings baked into the NEF file by the camera - only the Nikon software can interpret this correctly.
The momentary appearance of a more saturated image is the embedded jpeg with the settings, whereas the subsequent one is the true appearance of the raw image, without any in-camera tweaks. This is especially noticeable if you are using exaggerated Picture Control settings (e.g. Vivid or a setting with Saturation turned up).
I actually prefer the neutral result of the true raw image as it provides a lot more latitude for post-processing. I would prefer it that you didn't make sweeping statements on my behalf.